Step 1.
Create a bigNarrowPeak file. The first six fields of the bigNarrowPeak bed6+4 format are
described by the basic BED file format shown here.
You can also read about narrowPeak (or point-source peak),
the precursor to bigNarrowPeak, here.
Your bigNarrowPeak file must also contain the four extra fields described in the autoSql file definition
shown above: signalValue, pValue, qValue, peak.
Your bigNarrowPeak file must be sorted first on the chrom field, and
secondarily on the chromStart field. You can use the UNIX sort command to
do this:
sort -k1,1 -k2,2n unsorted.bed > input.bed
Step 2.
Download the bedToBigBed program from the
-binary utilities directory.
Step 3.
Use the fetchChromSizes script from the
-same directory to create a
+same directory to create a
chrom.sizes file for the UCSC database with which you are working (e.g., hg38).
Alternatively, you can download the chrom.sizes file for any assembly hosted at UCSC from
-our downloads page (click on "Full
+our downloads page (click on "Full
data set" for any assembly). For example, the hg38.chrom.sizes file for the hg38
database is located at
-http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes.
Step 4.
Create the bigNarrowPeak file from your sorted input file using the bedToBigBed
utility:
bedToBigBed -as=bigNarrowPeak.as -type=bed6+4 bigNarrowPeak.txt chrom.sizes myBigNarrowPeak.bbStep 5. Move the newly created bigNarrowPeak file (myBigNarrowPeak.bb) to a web-accessible http, https, or ftp location.
Step 6. Construct a custom track using a single track line. Note that any of the track attributes listed here are applicable to tracks of type bigNarrowPeak. The basic version of the track line will look something like this:
@@ -148,31 +148,31 @@After this example bigNarrowPeak track is loaded in the Genome Browser, click on a peak in the browser's track display to view the details page for that peak.
In this example, you will create your own bigNarrowPeak file from an existing bigNarrowPeak input file.
bedToBigBed
+ Download the bedToBigBed
utility (Step 2, above).bedToBigBed utility to create the bigNarrowPeak output file (step 4,
above):
bedToBigBed -type=bed6+4 -tab -as=bigNarrowPeak.as bigNarrowPeak.txt hg38.chrom.sizes bigNarrowPeak.bbIf you would like to share your bigNarrowPeak data track with a colleague, learn how to create a URL by looking at Example #6 on this page and the additional URL optional parameters section.
Because the bigNarrowPeak files are an extension of bigBed files, which are indexed binary files, it can be difficult to extract data from them. UCSC has developed the following programs to assist in working with bigBed formats, available from the -binary utilities directory.
+binary utilities directory.bigBedToBed — converts a bigBed file to ASCII BED format.bigBedSummary — extracts summary information from a bigBed
file.bigBedInfo — prints out information about a bigBed file.Such tools can be used to obtain only features within a given range, for example:
-bigBedToBed http://hgdownload.soe.ucsc.edu/gbdb/danRer10/transMap/V4/danRer10.refseq.transMapV4.bigPsl +bigBedToBed http://hgdownload.gi.ucsc.edu/gbdb/danRer10/transMap/V4/danRer10.refseq.transMapV4.bigPsl -chrom=chr6 -start=0 -end=1000000 stdout
As with all UCSC Genome Browser programs, type the program name (with no parameters) at the command line to view the usage statement.
If you encounter an error when you run the bedToBigBed program, check your input
file for data coordinates that extend past the end of the chromosome. If these are
present, run the bedClip program
-(available here) to remove the problematic
+(available here) to remove the problematic
row(s) before running the bedToBigBed program.